6TU6 | pdb_00006tu6

Kemp Eliminase HG3.17 mutant Q50M, E47N, N300D Complexed with Transition State Analog 6-Nitrobenzotriazole

PDB DOI: https://doi.org/10.2210/pdb6TU6/pdb

Classification: DE NOVO PROTEIN
Organism(s): synthetic construct
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2020-01-02 Released: 2020-04-01
Deposition Author(s): Bloch, J.S., Hilvert, D.
Funding Organization(s): Swiss National Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.05 Å
R-Value Free:
0.231 (Depositor), 0.230 (DCC)
R-Value Work:
0.196 (Depositor), 0.200 (DCC)
R-Value Observed:
0.196 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

Contribution of Oxyanion Stabilization to Kemp Eliminase Efficiencyproficiency

Kries, H., Bloch, J.S., Bunzel, H.A., Hilvert, D.

(2020) ACS Catal

DOI: https://doi.org/10.1021/acscatal.0c00575

Macromolecule Content

Total Structure Weight: 554.16 kDa
Atom Count: 45,872
Modeled Residue Count: 4,802
Deposited Residue Count: 5,072
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kemp Eliminase HG3.17 mutant Q50M, E47N, N300D Complexed with Transition State Analog 6-Nitrobenzotriazole	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	317	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6NT (Subject of Investigation/LOI) Query on 6NT Download Ideal Coordinates CCD File SDF format, chain BB [auth P] SDF format, chain CA [auth E] SDF format, chain FA [auth F] SDF format, chain HA [auth G] SDF format, chain IA [auth H] SDF format, chain LA [auth I] SDF format, chain OA [auth J] SDF format, chain Q [auth A] SDF format, chain QA [auth K] SDF format, chain RA [auth L] SDF format, chain S [auth B] SDF format, chain TA [auth M] SDF format, chain U [auth C] SDF format, chain WA [auth N] SDF format, chain Y [auth D] SDF format, chain ZA [auth O] MOL2 format, chain BB [auth P] MOL2 format, chain CA [auth E] MOL2 format, chain FA [auth F] MOL2 format, chain HA [auth G] MOL2 format, chain IA [auth H] MOL2 format, chain LA [auth I] MOL2 format, chain OA [auth J] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth K] MOL2 format, chain RA [auth L] MOL2 format, chain S [auth B] MOL2 format, chain TA [auth M] MOL2 format, chain U [auth C] MOL2 format, chain WA [auth N] MOL2 format, chain Y [auth D] MOL2 format, chain ZA [auth O] mmCIF format, chain BB [auth P] mmCIF format, chain CA [auth E] mmCIF format, chain FA [auth F] mmCIF format, chain HA [auth G] mmCIF format, chain IA [auth H] mmCIF format, chain LA [auth I] mmCIF format, chain OA [auth J] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth K] mmCIF format, chain RA [auth L] mmCIF format, chain S [auth B] mmCIF format, chain TA [auth M] mmCIF format, chain U [auth C] mmCIF format, chain WA [auth N] mmCIF format, chain Y [auth D] mmCIF format, chain ZA [auth O]	BB [auth P] CA [auth E] FA [auth F] HA [auth G] IA [auth H] BB [auth P], CA [auth E], FA [auth F], HA [auth G], IA [auth H], LA [auth I], OA [auth J], Q [auth A], QA [auth K], RA [auth L], S [auth B], TA [auth M], U [auth C], WA [auth N], Y [auth D], ZA [auth O]	6-NITROBENZOTRIAZOLE C₆ H₄ N₄ O₂ AOCDQWRMYHJTMY-UHFFFAOYSA-N		Interactions Focus chain BB [auth P] Focus chain CA [auth E] Focus chain FA [auth F] Focus chain HA [auth G] Focus chain IA [auth H] Focus chain LA [auth I] Focus chain OA [auth J] Focus chain Q [auth A] Focus chain QA [auth K] Focus chain RA [auth L] Focus chain S [auth B] Focus chain TA [auth M] Focus chain U [auth C] Focus chain WA [auth N] Focus chain Y [auth D] Focus chain ZA [auth O] Interactions & Density Focus chain BB [auth P] Focus chain CA [auth E] Focus chain FA [auth F] Focus chain HA [auth G] Focus chain IA [auth H] Focus chain LA [auth I] Focus chain OA [auth J] Focus chain Q [auth A] Focus chain QA [auth K] Focus chain RA [auth L] Focus chain S [auth B] Focus chain TA [auth M] Focus chain U [auth C] Focus chain WA [auth N] Focus chain Y [auth D] Focus chain ZA [auth O]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain AB [auth O] SDF format, chain BA [auth D] SDF format, chain CB [auth P] SDF format, chain DA [auth E] SDF format, chain DB [auth P] SDF format, chain EA [auth E] SDF format, chain GA [auth F] SDF format, chain JA [auth H] SDF format, chain KA [auth H] SDF format, chain MA [auth I] SDF format, chain NA [auth I] SDF format, chain PA [auth J] SDF format, chain R [auth A] SDF format, chain SA [auth L] SDF format, chain T [auth B] SDF format, chain UA [auth M] SDF format, chain V [auth C] SDF format, chain VA [auth M] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain XA [auth N] SDF format, chain YA [auth N] SDF format, chain Z [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain AB [auth O] MOL2 format, chain BA [auth D] MOL2 format, chain CB [auth P] MOL2 format, chain DA [auth E] MOL2 format, chain DB [auth P] MOL2 format, chain EA [auth E] MOL2 format, chain GA [auth F] MOL2 format, chain JA [auth H] MOL2 format, chain KA [auth H] MOL2 format, chain MA [auth I] MOL2 format, chain NA [auth I] MOL2 format, chain PA [auth J] MOL2 format, chain R [auth A] MOL2 format, chain SA [auth L] MOL2 format, chain T [auth B] MOL2 format, chain UA [auth M] MOL2 format, chain V [auth C] MOL2 format, chain VA [auth M] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain XA [auth N] MOL2 format, chain YA [auth N] MOL2 format, chain Z [auth D] mmCIF format, chain AA [auth D] mmCIF format, chain AB [auth O] mmCIF format, chain BA [auth D] mmCIF format, chain CB [auth P] mmCIF format, chain DA [auth E] mmCIF format, chain DB [auth P] mmCIF format, chain EA [auth E] mmCIF format, chain GA [auth F] mmCIF format, chain JA [auth H] mmCIF format, chain KA [auth H] mmCIF format, chain MA [auth I] mmCIF format, chain NA [auth I] mmCIF format, chain PA [auth J] mmCIF format, chain R [auth A] mmCIF format, chain SA [auth L] mmCIF format, chain T [auth B] mmCIF format, chain UA [auth M] mmCIF format, chain V [auth C] mmCIF format, chain VA [auth M] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C] mmCIF format, chain XA [auth N] mmCIF format, chain YA [auth N] mmCIF format, chain Z [auth D]	AA [auth D] AB [auth O] BA [auth D] CB [auth P] DA [auth E] AA [auth D], AB [auth O], BA [auth D], CB [auth P], DA [auth E], DB [auth P], EA [auth E], GA [auth F], JA [auth H], KA [auth H], MA [auth I], NA [auth I], PA [auth J], R [auth A], SA [auth L], T [auth B], UA [auth M], V [auth C], VA [auth M], W [auth C], X [auth C], XA [auth N], YA [auth N], Z [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth D] Focus chain AB [auth O] Focus chain BA [auth D] Focus chain CB [auth P] Focus chain DA [auth E] Focus chain DB [auth P] Focus chain EA [auth E] Focus chain GA [auth F] Focus chain JA [auth H] Focus chain KA [auth H] Focus chain MA [auth I] Focus chain NA [auth I] Focus chain PA [auth J] Focus chain R [auth A] Focus chain SA [auth L] Focus chain T [auth B] Focus chain UA [auth M] Focus chain V [auth C] Focus chain VA [auth M] Focus chain W [auth C] Focus chain X [auth C] Focus chain XA [auth N] Focus chain YA [auth N] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain AB [auth O] Focus chain BA [auth D] Focus chain CB [auth P] Focus chain DA [auth E] Focus chain DB [auth P] Focus chain EA [auth E] Focus chain GA [auth F] Focus chain JA [auth H] Focus chain KA [auth H] Focus chain MA [auth I] Focus chain NA [auth I] Focus chain PA [auth J] Focus chain R [auth A] Focus chain SA [auth L] Focus chain T [auth B] Focus chain UA [auth M] Focus chain V [auth C] Focus chain VA [auth M] Focus chain W [auth C] Focus chain X [auth C] Focus chain XA [auth N] Focus chain YA [auth N] Focus chain Z [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.05 Å
R-Value Free: 0.231 (Depositor), 0.230 (DCC)
R-Value Work: 0.196 (Depositor), 0.200 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.37	α = 88.527
b = 108.69	β = 90.155
c = 108.72	γ = 89.818

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-04-01

Deposition Author(s):

Bloch, J.S.

Hilvert, D.

Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	--

Revision History (Full details and data files)

Version 1.0: 2020-04-01
Type: Initial release
Version 2.0: 2020-11-18
Changes: Advisory, Atomic model, Data collection, Derived calculations
Version 2.1: 2024-01-24
Changes: Data collection, Database references, Refinement description
Version 2.2: 2024-11-20
Changes: Structure summary